Make Links - Object Data Causes wild results
They are not disappeared, but they are all at the same place as HiPoly :)

Problem here is you applied Rot and Loc, that are zero now for each object origin, but their Object data are not. That means if you Ctrl+L > Object Data to each object it copy exactly the same.

To fix Location is not a problem just select all, search for Set Origin > Origin to Geometry. But how to restore Rotation I don't know.

If you have a version before applied transform, would be better.